The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

Arun Prasad Pandurangan, Jonathan Stahlhacke, Matt E. Oates, Ben Smithers, Julian Gough

Research output: Contribution to journalArticle (Academic Journal)peer-review

26 Citations (Scopus)
213 Downloads (Pure)

Abstract

Here, we present a major update to the SUPERFAMILY database and the webserver. We describe the addition of new SUPERFAMILY 2.0 profile HMM library containing a total of 27 623 HMMs. The database now includes Superfamily domain annotations for millions of protein sequences taken from the Universal Protein Recourse Knowledgebase (UniProtKB) and the National Center for Biotechnology Information (NCBI). This addition constitutes about 51 and 45 million distinct protein sequences obtained from UniProtKB and NCBI respectively. Currently, the database contains annotations for 63 244 and 102 151 complete genomes taken from UniProtKB and NCBI respectively. The current sequence collection and genome update is the biggest so far in the history of SUPERFAMILY updates. In order to the deal with the massive wealth of information, here we introduce a new SUPERFAMILY 2.0 webserver (http://supfam.org). Currently, the webserver mainly focuses on the search, retrieval and display of Superfamily annotation for the entire sequence and genome collection in the database.

Original languageEnglish
Pages (from-to)D490-D494
Number of pages5
JournalNucleic Acids Research
Volume47
Issue numberD1
Early online date16 Nov 2018
DOIs
Publication statusPublished - 8 Jan 2019

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